diff Group.py @ 0:57299471d6c1 draft default tip

planemo upload commit 402a746f69e9f1dbb57007536fc36dc6ce3180de

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Group.py	Wed Apr 12 17:37:47 2017 -0400
@@ -0,0 +1,59 @@
+from operator import itemgetter
+
+# Input: A group: a list that contains lines belonging to the same gene
+class Group:
+    # Modify "type" column and "attributes" colunm, initialize id, gene, source, stream
+    def __init__(self, group):
+        self.group = group
+        self.id = str(group[0][0])
+        self.source = str(group[0][1])
+        self.stream = str(group[0][6])
+        self.gene = str(group[0][8])
+        for x in range(0, len(group)):
+            self.group[x][2] = "CDS"
+            self.group[x][8] = "Parent=mRNA_" + self.gene
+            self.group[x][3] = int(self.group[x][3])
+            self.group[x][4] = int(self.group[x][4])
+
+    # Order the group elements accoriding to Stream, +: ascanding order, -: descanding order   
+    def order(self):
+        self.num = len(self.group)
+        if self.stream == "+":
+            self.group = sorted(self.group, key=itemgetter(3))
+            self.min_item = self.group[0][3]
+            self.max_item = self.group[self.num-1][4]
+        elif self.stream == "-":
+            self.group = sorted(self.group, key=itemgetter(3), reverse=True)
+            self.min_item = self.group[self.num-1][3]
+            self.max_item = self.group[0][4]
+        else:
+            print("Stream in invalid!\n")
+    
+    def phaseCalculator(self, i, donor = 0):
+        if i >= self.num:
+            pass
+        else:
+            self.type = self.group[i][2]
+            self.size = self.group[i][4] - self.group[i][3] + 1
+        if self.num == 1:
+            if self.type == "Eterm":
+                self.group[i][7] = str(self.size % 3)
+            else:
+                self.group[i][7] = "0"
+        elif self.num > 1 and i < self.num:
+            accept = (3 - donor) % 3
+            self.group[i][7] = str(accept)
+            donor = (self.size - accept) % 3
+            i = i + 1
+            self.phaseCalculator(i, donor)
+            
+    
+    def writer(self, gff3):
+        self.order()
+        self.phaseCalculator(0)
+        gff3.write(self.id + "\t" + self.source + "\tgene\t" + str(self.min_item) + "\t" + str(self.max_item) + "\t.\t" + self.stream + "\t.\t" + "ID=" + self.gene + "\n")
+        gff3.write(self.id + "\t" + self.source + "\tmRNA\t" + str(self.min_item) + "\t" + str(self.max_item) + "\t.\t" + self.stream + "\t.\t" + "ID=mRNA_" + self.gene + ";Parent=" + self.gene + "\n")
+        for x in range(0, len(self.group)):
+            self.group[x][3] = str(self.group[x][3])
+            self.group[x][4] = str(self.group[x][4])
+            gff3.write("\t".join(self.group[x]) + "\n")
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